.TH g_clustsize 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_clustsize - calculate size distributions of atomic clusters

.B VERSION 4.5
.SH SYNOPSIS
\f3g_clustsize\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " csize.xpm "
.BI "\-ow" " csizew.xpm "
.BI "\-nc" " nclust.xvg "
.BI "\-mc" " maxclust.xvg "
.BI "\-ac" " avclust.xvg "
.BI "\-hc" " histo\-clust.xvg "
.BI "\-temp" " temp.xvg "
.BI "\-mcn" " maxclust.ndx "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-tu" " enum "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-cut" " real "
.BI "\-[no]mol" ""
.BI "\-[no]pbc" ""
.BI "\-nskip" " int "
.BI "\-nlevels" " int "
.BI "\-ndf" " int "
.BI "\-rgblo" " vector "
.BI "\-rgbhi" " vector "
.SH DESCRIPTION
\&This program computes the size distributions of molecular/atomic clusters in
\&the gas phase. The output is given in the form of a XPM file.
\&The total number of clusters is written to a XVG file.


\&When the \fB \-mol\fR option is given clusters will be made out of
\&molecules rather than atoms, which allows clustering of large molecules.
\&In this case an index file would still contain atom numbers
\&or your calculation will die with a SEGV.


\&When velocities are present in your trajectory, the temperature of
\&the largest cluster will be printed in a separate xvg file assuming
\&that the particles are free to move. If you are using constraints,
\&please correct the temperature. For instance water simulated with SHAKE
\&or SETTLE will yield a temperature that is 1.5 times too low. You can
\&compensate for this with the \-ndf option. Remember to take the removal
\&of center of mass motion into account.


\&The \fB \-mc\fR option will produce an index file containing the
\&atom numbers of the largest cluster.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input, Opt.
 Portable xdr run input file 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " csize.xpm" 
.B Output
 X PixMap compatible matrix file 

.BI "\-ow" " csizew.xpm" 
.B Output
 X PixMap compatible matrix file 

.BI "\-nc" " nclust.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-mc" " maxclust.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-ac" " avclust.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-hc" " histo\-clust.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-temp" " temp.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-mcn" " maxclust.ndx" 
.B Output, Opt.
 Index file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-cut"  " real" " 0.35  " 
 Largest distance (nm) to be considered in a cluster

.BI "\-[no]mol"  "no    "
 Cluster molecules rather than atoms (needs tpr file)

.BI "\-[no]pbc"  "yes   "
 Use periodic boundary conditions

.BI "\-nskip"  " int" " 0" 
 Number of frames to skip between writing

.BI "\-nlevels"  " int" " 20" 
 Number of levels of grey in xpm output

.BI "\-ndf"  " int" " \-1" 
 Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used.

.BI "\-rgblo"  " vector" " 1 1 0" 
 RGB values for the color of the lowest occupied cluster size

.BI "\-rgbhi"  " vector" " 0 0 1" 
 RGB values for the color of the highest occupied cluster size

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
